3DNA: A Tool for Sculpting Brick-Based DNA Nanostructures

Abstract

To assist in the speed and accuracy of designing brick-based DNA nanostructures, we introduce a lightweight software suite 3DNA that can be used to generate complex structures. Currently, implementation of this fabrication strategy involves working with generalized, typically commercial CAD software, ad-hoc sequence-generating scripts, and visualization software, which must often be integrated together with an experimental lab setup for handling the hundreds or thousands of constituent DNA sequences. 3DNA encapsulates the solutions to these challenges in one package by providing a customized, easy-to-use molecular canvas and back-end functionality to assist in both visualization and sequence design. The primary motivation behind this software is enabling broader use of the brick-based method for constructing rigid, 3D DNA-based nanostructures, first introduced in 2012. 3DNA is developed to provide a streamlined, real-time workflow for designing and implementing this type of 3D nanostructure by integrating different visualization and design modules. Due to its cross-platform nature, it can be used on the most popular desktop environments, i.e., Windows, Mac OS X, and various flavors of Linux. 3DNA utilizes toolbar-based navigation to create a user-friendly GUI and includes a customized feature to analyze the constituent DNA sequences. Finally, the oligonucleotide sequences themselves can either be created on the fly by a random sequence generator, or selected from a pre-existing set of sequences making up a larger molecular canvas.